Or i have alzheimer or my tri matrix emblem disappear somehow. Is it that possible?

On two occasions, i've used Tri-Emblems and my Energy, Shield and Hull didn't replenish while i was under attack by another player. Were you under attack when using the artifact?

No i didn't. i was few hundred experience points from level up so i was waiting to recharge my energy, to level up, spend energy and then use 'matrix' to level up one more. Hmmm very weird situation but I can live with it if it happened the first and only time.